The controversial cleric is serving a 15-year jail term for funding and supporting a terrorist training camp in Indonesia's Aceh province.

On Thursday, he was allowed a day trip from Gunung Sindur prison in Bogor, West Java, to a hospital in Jakarta for treatment over his declining health.

Bashir, who will be 80 in August, had pooling of blood in the legs, otherwise known as chronic venous insufficiency, or weak blood circulation.

His son, Abu Rochim Bashir, said his father's condition had been worsening since last year, and that he also suffered from cardiovascular disease and had gastric pains.

Indonesian media reports said the son sent a letter to Indonesian Defence Minister Ryamizard Ryacudu on Thursday, applying for his father to be transferred to house detention at his home in Solo, Central Java.

The minister indicated he supported home detention, so Bashir could be cared for by his family, or at the very least a transfer to a prison closer to his home town.

"The President is very concerned. Abu Bakar Bashir is old, sick, his feet are swollen. If anything happened to him in prison what will the world say? So in the name of humanity, I told the President that he should be moved somewhere near Solo."

One Muslim leader, Ulema Council chairman Maaruf Amin, has argued Bashir deserved clemency because of his age and poor health.

Indonesia's top security minister, Wiranto, said government ministers and police would soon meet to discuss Bashir's future and make a recommendation to Indonesian President Joko 'Jokowi' Widodo.

"Clemency, pardon, house arrest or just hospital treatment. It will be discussed in the near future and will be reported to the President," Wiranto said.

Bashir's many sympathisers hoped the President would agree to grant him permanent release — a move that would strengthen Joko Widodo's standing among hard-line Muslims in the lead-up to next year's presidential elections.

A presidential spokesman confirmed house arrest was "possible under the law".

However, a presidential pardon would first require Bashir to apply for clemency, which in Indonesia would require him to admit guilt, something his lawyer ruled out.

"If he conveys a clemency, it means he is sorry," Guntur Fattahillah told reporters at Cipto Mangunkusumo Hospital on Thursday.

Bashir has always maintained his innocence.

When he was sentenced in 2011, he said he rejected the conviction because it was based on 'infidel' law.

At his trial, he denied having any links to the training camp in Aceh, and said the group he founded in 2008, Jemaah Ansharut Tauhid was a legitimate Islamic organisation.

Clemency or even house arrest would likely draw criticism from Indonesia's allies, including Australia and the United States, given the support Bashir still has among Islamist sympathisers, and the message it would send in a country where jihadist extremism remains high.

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